#229 Fix DCD reading for versions > 13.0.8

[Sergio Martí]

Version 13.0.8 is the last from which i am able to load DCD files with the command:
load trajectory "x.pdb" coord "x.dcd"

after playing a bit with the jsmol version, i think the problem could be related with the endianness
(which defaults to big, although it is a little-endian binary file...)

see about line 25 of BinaryDcdReader.js:

var n = this.binaryDoc.readInt ();
alert( n ); // displays 1409286144 instead of 84
this.binaryDoc.setStream (this.vwr.getJzt (), null, n != 0x54);
alert( this.binaryDoc.isBigEndian ); // displays true

and changing to:

var n = this.binaryDoc.readLEInt ();
alert( n ); // displays 84
this.binaryDoc.setStream (this.vwr.getJzt (), null, n != 0x54);
alert( this.binaryDoc.isBigEndian ); // displays false

but then there is an extra error...

InternalError: size and count too large try/catch path:
0 function (b,d)
args[0]=InternalError: size and count too large
args[1]=function (){a.instantialize(this,arguments)}
1 J.adapter.readers.more.BinaryDcdReader.getTrajectoryStep(trajectoryStep)
args[0]=,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,...
2 J.adapter.readers.more.BinaryDcdReader.readCoordinates()
3 J.adapter.readers.more.BinaryDcdReader.processBinaryDocument()
4 J.adapter.smarter.AtomSetCollectionReader.readData()
5 J.adapter.smarter.SmarterJmolAdapter.getAtomSetCollectionReaders(a,
c,d,b,f)
args[0]=[J.io.FilesReader object]
args[1]=file:/tmp/jmol/x.pdb,file:/tmp/jmol/x.dcd
args[2]=,
args[3]={fileTypes=, fullPathNames=file:/tmp/jmol/x.pdbfile:/tmp/jmo...
args[4]=false
6 J.io.FilesReader.run()
7 JV.FileManager.createAtomSetCollectionFromFiles(a,
c,b)
args[0]=[J.io.FilesReader object]
args[1]={fileTypes=, fullPathNames=file:/tmp/jmol/x.pdbfile:/tmp/jmo...
args[2]=false
8 JV.Viewer.loadModelFromFile(a,c,b,e,f,g,h,k,l,n)
args[0]=1448924482577
args[1]=fileSet
args[2]=file:/tmp/jmol/x.pdb,file:/tmp/jmol/x.dcd
args[3]=null
args[4]=false
args[5]={fileTypes=, fullPathNames=file:/tmp/jmol/x.pdbfile:/tmp/jmo...
args[6]=load trajectory /file/$FILENAME1$ COORD {0 -1 1} /file/$...
args[7]=
args[8]=0
args[9]=false
9 JS.ScriptEval.cmdLoad()

Any ideas?

[Bob Hanson]

Please send me a sample file -- hansonr@stolaf.edu

[Angel Herraez]

Abandoned thread.